Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques

Microsecond Timescale Conformational Dynamics of a Small-Molecule Ligand within the Active Site of a Protein

The possible internal dynamics of non-isotope-labeled small-molecule ligands inside a target protein is inherently difficult to capture. Whereas high crystallographic temperature factors can denote either static disorder or motion, even moieties with very low B-factors can be subject to vivid motion between symmetry-related sites. Here we report the experimental identification of internal μs timescale dynamics of a high-affinity, natural-abundance ligand tightly bound to the enzyme human carbonic anhydrase II (hCAII) even within a crystalline lattice. The rotamer jumps of the ligand's benzene group manifest themselves both, in solution and fast magic-angle spinning solid-state NMR 1 H R1ρ relaxation dispersion, for which we obtain further mechanistic insights from molecular-dynamics (MD) simulations. The experimental confirmation of rotameric jumps in bound ligands within proteins in solution or the crystalline state may improve understanding of host-guest interactions in biology and supra-molecular chemistry and may facilitate medicinal chemistry for future drug campaigns.

Dealing with Induced Fit, Conformational Selection, and Secondary Poses in Molecular Dynamics Simulations for Reliable Free Energy Predictions

In this study, we have tested the performance of standard molecular dynamics (MD) simulations, replicates of shorter standard MD simulations, and Hamiltonian Replica Exchange (HREM) simulations for the sampling of two macrocyclic hosts for guest delivery, characterized by induced fit (phenyl-based host) and conformation selection (naphthyl-based host) and of the ODR-BRD4(I) drug-receptor system where the ligand can assume two main poses. For the optimization of the HREM simulation, we have proposed and tested an on-the-fly iterative scheme for equalizing the acceptance ratio along the replica progression at a constant replica number resulting in a moderate impact of the sampling efficiency. Concerning standard MD, we have found that, while splitting the total allocated simulation time in short MD replicates can reproduce the sampling efficiency of HREM in the phenyl-based host and in the ODR-BRD4(I) complex, in the naphthyl-based macrocycle, characterized by long-lived metastable states, enhanced sampling techniques are the only viable alternative for a reliable canonical sampling of the rugged conformational landscape.

5D solid-state NMR spectroscopy for facilitated resonance assignment

1H-detected solid-state NMR spectroscopy has been becoming increasingly popular for the characterization of protein structure, dynamics, and function. Recently, we showed that higher-dimensionality solid-state NMR spectroscopy can aid resonance assignments in large micro-crystalline protein targets to combat ambiguity (Klein et al., Proc. Natl. Acad. Sci. U.S.A. 2022). However, assignments represent both, a time-limiting factor and one of the major practical disadvantages within solid-state NMR studies compared to other structural-biology techniques from a very general perspective. Here, we show that 5D solid-state NMR spectroscopy is not only justified for high-molecular-weight targets but will also be a realistic and practicable method to streamline resonance assignment in small to medium-sized protein targets, which such methodology might not have been expected to be of advantage for. Using a combination of non-uniform sampling and the signal separating algorithm for spectral reconstruction on a deuterated and proton back-exchanged micro-crystalline protein at fast magic-angle spinning, direct amide-to-amide correlations in five dimensions are obtained with competitive sensitivity compatible with common hardware and measurement time commitments. The self-sufficient backbone walks enable efficient assignment with very high confidence and can be combined with higher-dimensionality sidechain-to-backbone correlations from protonated preparations into minimal sets of experiments to be acquired for simultaneous backbone and sidechain assignment. The strategies present themselves as potent alternatives for efficient assignment compared to the traditional assignment approaches in 3D, avoiding user misassignments derived from ambiguity or loss of overview and facilitating automation. This will ease future access to NMR-based characterization for the typical solid-state NMR targets at fast MAS.

Protein dynamics detected by magic-angle spinning relaxation dispersion NMR

Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies.

Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins

We demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.

Microsecond Motion of the Bacterial Transporter EmrE in Lipid Bilayers

The bacterial transporter EmrE is a homo-dimeric membrane protein that effluxes cationic polyaromatic substrates against the concentration gradient by coupling to proton transport. As the archetype of the small multidrug resistance family of transporters, EmrE structure and dynamics provide atomic insights into the mechanism of transport by this family of proteins. We recently determined high-resolution structures of EmrE in complex with a cationic substrate, tetra(4-fluorophenyl)phosphonium (F4-TPP+), using solid-state NMR spectroscopy and an S64V-EmrE mutant. The substrate-bound protein exhibits distinct structures at acidic and basic pH, reflecting changes upon binding or release of a proton from residue E14, respectively. To obtain insight into the protein dynamics that mediate substrate transport, here we measure 15N rotating-frame spin-lattice relaxation (R1ρ) rates of F4-TPP+-bound S64V-EmrE in lipid bilayers under magic-angle spinning (MAS). Using perdeuterated and back-exchanged protein and 1H-detected 15N spin-lock experiments under 55 kHz MAS, we measured 15N R1ρ rates site-specifically. Many residues show spin-lock field-dependent 15N R1ρ relaxation rates. This relaxation dispersion indicates the presence of backbone motions at a rate of about 6000 s-1 at 280 K for the protein at both acidic and basic pH. This motional rate is 3 orders of magnitude faster than the alternating access rate but is within the range estimated for substrate binding. We propose that these microsecond motions may allow EmrE to sample different conformations to facilitate substrate binding and release from the transport pore.

Integrated Assessment of the Structure and Dynamics of Solid Proteins

Understanding macromolecular function, interactions, and stability hinges on detailed assessment of conformational ensembles. For solid proteins, accurate elucidation of the spatial aspects of dynamics at physiological temperatures is limited by the qualitative character or low abundance of solid-state nuclear magnetic resonance internuclear distance information. Here, we demonstrate access to abundant proton-proton internuclear distances for integrated structural biology and chemistry with unprecedented accuracy. Apart from highest-resolution single-state structures, the exact distances enable molecular dynamics (MD) ensemble simulations orchestrated by a dense network of experimental interproton distance boundaries gathered in the context of their physical lattices. This direct embedding of experimental ensemble distances into MD will provide access to representative, atomic-level spatial details of conformational dynamics in supramolecular assemblies, crystalline and lipid-embedded proteins, and beyond.

Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD

Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein's hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine ¹H-¹³C/²H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10-20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.

Rotating Frame Relaxation in Magic Angle Spinning Solid State NMR, a Promising Tool for Characterizing Biopolymer Motion

Magic angle spinning NMR rotating frame relaxation measurements provide a unique experimental window into biomolecules dynamics, as is illustrated by numerous recent applications. We discuss experimental strategies for this class of experiments, with a particular focus on systems where motion-driven modulation of the chemical shift interaction is the main mechanism for relaxation. We also explore and describe common strategies for interpreting the data sets to extract motion time scale, activation energy, and angle or order parameters from rotating frame relaxation data. Using model free analysis and numerical simulations, including time domain treatment, we explore conditions under which it is possible to obtain accurate and precise information about the time scales of motions. Overall, with rapid technical advances in solid state NMR, there is a bright future for this class of studies.

Fast Magic‐Angle‐Spinning NMR Reveals the Evasive Hepatitis B Virus Capsid C‐Terminal Domain**

Experimentally determined protein structures often feature missing domains. One example is the C‐terminal domain (CTD) of the hepatitis B virus capsid protein, a functionally central part of this assembly, crucial in regulating nucleic‐acid interactions, cellular trafficking, nuclear import, particle assembly and maturation. However, its structure remained elusive to all current techniques, including NMR. Here we show that the recently developed proton‐detected fast magic‐angle‐spinning solid‐state NMR at >100 kHz MAS allows one to detect this domain and unveil its structural and dynamic behavior. We describe the experimental framework used and compare the domain's behavior in different capsid states. The developed approaches extend solid‐state NMR observations to residues characterized by large‐amplitude motion on the microsecond timescale, and shall allow one to shed light on other flexible protein domains still lacking their structural and dynamic characterization.

1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning

Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.

Deuteron rotating frame relaxation for the detection of slow motions in rotating solids

We demonstrate experimental and computational approaches for measuring ²H rotating frame NMR relaxation for solid samples under magic angle spinning (MAS) conditions. The relaxation properties of the deuterium spin-1 system are dominated by the reorientation of the anisotropic quadrupolar tensors, with the effective quadrupolar coupling constant around 55 kHz for methyl groups. The technique is demonstrated using the model compound dimethyl-sulfone at MAS rates of 10 and 60 kHz as well as for an amyloid fibril sample comprising an amyloid-β (1-40) protein with a selective methyl group labeled in the disordered domain of the fibrils, at an MAS rate of 8 kHz. For both systems, the motional parameters fall well within the ranges determined by other techniques, thus validating its feasibility. Experimental and computational factors such as i) the probe's radio frequency inhomogeneity profiles, ii) rotary resonances at conditions for which the spin-lock field strength matches the half- or full-integer of the MAS rate, iii) the choice of MAS rates and spin-lock field strengths, and iv) simulations that account for the interconversion of multiple coherences for the spin-1 system under MAS and deviations from the analytical Redfield treatment are thoroughly considered.

Solid-State NMR: Methods for Biological Solids

In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.

Unambiguous Side-Chain Assignments for Solid-State NMR Structure Elucidation of Nondeuterated Proteins via a Combined 5D/4D Side-Chain-to-Backbone Experiment

Owing to fast-magic-angle-spinning technology, proton-detected solid-state NMR has been facilitating the analysis of insoluble, crystalline, sedimented, and membrane proteins. However, potential applications have been largely restricted by limited access to side-chain resonances. The recent availability of spinning frequencies exceeding 100 kHz in principle now allows direct probing of all protons without the need for partial deuteration. This potentiates both the number of accessible target proteins and possibilities to exploit side-chain protons as reporters on distances and interactions. Their low dispersion, however, has severely compromised their chemical-shift assignment, which is a prerequisite for their use in downstream applications. Herein, we show that unambiguous correlations are obtained from 5D methodology by which the side-chain resonances are directly connected with the backbone. When further concatenated with simultaneous 4D intra-side-chain correlations, this yields comprehensive assignments in the side chains and hence allows a high density of distance restraints for high-resolution structure calculation from minimal amounts of protein.

Experimental Characterization of the Hepatitis B Virus Capsid Dynamics by Solid-State NMR

Protein plasticity and dynamics are important aspects of their function. Here we use solid-state NMR to experimentally characterize the dynamics of the 3.5 MDa hepatitis B virus (HBV) capsid, assembled from  240 copies of the Cp149 core protein. We measure both T₁ and T_1ρ relaxation times, which we use to establish detectors on the nanosecond and microsecond timescale. We compare our results to those from a 1 microsecond all-atom Molecular Dynamics (MD) simulation trajectory for the capsid. We show that, for the constituent residues, nanosecond dynamics are faithfully captured by the MD simulation. The calculated values can be used in good approximation for the NMR-non-detected residues, as well as to extrapolate into the range between the nanosecond and microsecond dynamics, where NMR has a blind spot at the current state of technology. Slower motions on the microsecond timescale are difficult to characterize by all-atom MD simulations owing to computational expense, but are readily accessed by NMR. The two methods are, thus, complementary, and a combination thereof can reliably characterize motions covering correlation times up to a few microseconds.

Deuteration for High-Resolution Detection of Protons in Protein Magic Angle Spinning (MAS) Solid-State NMR

Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B₀ field in a perdeuterated environment are compiled.

Towards a native environment: structure and function of membrane proteins in lipid bilayers by NMR

Solid-state NMR (ssNMR) is a versatile technique that can be used for the characterization of various materials, ranging from small molecules to biological samples, including membrane proteins. ssNMR can probe both the structure and dynamics of membrane proteins, revealing protein function in a near-native lipid bilayer environment. The main limitation of the method is spectral resolution and sensitivity, however recent developments in ssNMR hardware, including the commercialization of 28 T magnets (1.2 GHz proton frequency) and ultrafast MAS spinning (<100 kHz) promise to accelerate acquisition, while reducing sample requirement, both of which are critical to membrane protein studies. Here, we review recent advances in ssNMR methodology used for structure determination of membrane proteins in native and mimetic environments, as well as the study of protein functions such as protein dynamics, and interactions with ligands, lipids and cholesterol.

Backbone assignment of crystalline E. coli maltose binding protein

The E.coli maltose binding protein (MBP) is a 42.5 kDa molecule widely employed in many biotechnology applications. Because of its molecular size, it has become the main model system for the development of solution NMR methods adapted to large biomolecular targets. Here, we report virtually complete (~ 90%) backbone resonance assignments obtained on a microcrystalline sample of MBP with ¹H-detected solid-state NMR at fast (> 100 kHz) magic-angle spinning. We additionally present the detailed description of the methodology employed for the preparation of the sample and the acquisition and analysis of the NMR spectra. The chemical shifts, obtained with a single uniformly ¹⁵N, ¹³C-labelled and fully-protonated sample and about 2 weeks on a 800 MHz NMR spectrometer, have been deposited to the BMRB under the accession number 50089.

Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches

Out-of-equilibrium processes are ubiquitous across living organisms and all structural hierarchies of life. At the molecular scale, out-of-equilibrium processes (for example, enzyme catalysis, gene regulation, and motor protein functions) cause biological macromolecules to sample an ensemble of conformations over a wide range of time scales. Quantifying and conceptualizing the structure–dynamics to function relationship is challenging because continuously evolving multidimensional energy landscapes are necessary to describe nonequilibrium biological processes in biological macromolecules. In this perspective, we explore the challenges associated with state-of-the-art experimental techniques to understanding biological macromolecular function. We argue that it is time to revisit how we probe and model functional out-of-equilibrium biomolecular dynamics. We suggest that developing integrated single-molecule multiparametric force–fluorescence instruments and using advanced molecular dynamics simulations to study out-of-equilibrium biomolecules will provide a path towards understanding the principles of and mechanisms behind the structure–dynamics to function paradigm in biological macromolecules.

Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase

The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.

Deuteron Chemical Exchange Saturation Transfer for the Detection of Slow Motions in Rotating Solids

We utilized the ²H Chemical Exchange Saturation Transfer (CEST) technique under magic angle spinning (MAS) conditions to demonstrate the feasibility of the method for studies of slow motions in the solid state. For the quadrupolar anisotropic interaction, the essence of CEST is to scan the saturation pattern over a range of offsets corresponding to the entire spectral region(s) for all conformational states involved, which translates into a range of −60–+ 60 kHz for methyl groups. Rotary resonances occur when the offsets are at half-and full-integer of the MAS rates. The choice of the optimal MAS rate is governed by the condition to reduce the number of rotary resonances in the CEST profile patterns and retain a sufficiently large quadrupolar interaction active under MAS to maintain sensitivity to motions. As examples, we applied this technique to a well-known model compound dimethyl-sulfone (DMS) as well as amyloid-β fibrils selectively deuterated at a single methyl group of A2 belonging to the disordered domain. It is demonstrated that the obtained exchange rate between the two rotameric states of DMS at elevated temperatures fell within known ranges and the fitted model parameters for the fibrils agree well with the previously obtained value using static ²H NMR techniques. Additionally, for the fibrils we have observed characteristic broadening of rotary resonances in the presence of conformational exchange, which provides implications for model selection and refinement. This work sets the stage for future potential extensions of the ²H CEST under MAS technique to multiple-labeled samples in small molecules and proteins.

Dynamics of uniformly labelled solid proteins between 100 and 300 K: A 2D 2H-13C MAS NMR approach

We describe a ²H based MAS nuclear magnetic resonance (NMR) method to obtain site-specific molecular dynamics of biomolecules. The method utilizes the use of deuterium nucleus as a spin label that is proven to be very useful in dynamics studies of solid biological and functional materials. The aim is to understand overall characteristics of protein backbone and side-chain motions for CD₃, CD₂ and CD groups, in terms of timescale, type and activation energy of the underlying processes. Variable temperature two-dimensional (2D) ²H-¹³C correlation MAS NMR spectra were recorded for the uniformly ²H,¹³C,¹⁵N labelled Alanine and microcrystalline SH3 at a broad temperature range, from 320 K down to 100 K. First, the deuterium quadrupolar-coupling constant from specific D-C sites is obtained with the 2D experiment by utilizing carbon chemical shifts. Second, the static quadrupolar patterns are obtained at 100 K. Third, variable temperature approach enabled the observation of quadrupolar pattern over different motional regimes; slow, intermediate and fast. And finally, the apparent activation energies for C-D sites are determined and compared, by evaluating the temperature induced signal intensities. This information led to the determination of the dynamic processes for different D-C sites at a broad range of temperature and motional timescales. This is a first representation of 2D ²H-¹³C MAS NMR approach applied to fully isotope labelled deuterated protein covering 220 K temperature range.

Protein structural dynamics by Magic-Angle Spinning NMR

Magic-Angle Spinning (MAS) Nuclear Magnetic Resonance (NMR) is a fast-developing technique, capable of complementing solution NMR, X-ray crystallography, and electron microscopy for the biophysical characterization of microcrystalline, poorly crystalline or disordered protein samples, such as enzymes, biomolecular assemblies, membrane-embedded systems or fibrils. Beyond structures, MAS NMR is an ideal tool for the investigation of dynamics, since it is unique in its ability to distinguish static and dynamic disorder, and to characterize not only amplitudes but also timescales of motion. Building on seminal work on model proteins, the technique is now ripe for widespread application in structural biology. This review briefly summarizes the recent evolutions in biomolecular MAS NMR and accounts for the growing number of systems where this spectroscopy has provided a description of conformational dynamics over the very last few years.

Water orientation and dynamics in the closed and open influenza B virus M2 proton channels

The influenza B M2 protein forms a water-filled tetrameric channel to conduct protons across the lipid membrane. To understand how channel water mediates proton transport, we have investigated the water orientation and dynamics using solid-state NMR spectroscopy and molecular dynamics (MD) simulations. 13C-detected water 1H NMR relaxation times indicate that water has faster rotational motion in the low-pH open channel than in the high-pH closed channel. Despite this faster dynamics, the open-channel water shows higher orientational order, as manifested by larger motionally-averaged 1H chemical shift anisotropies. MD simulations indicate that this order is induced by the cationic proton-selective histidine at low pH. Furthermore, the water network has fewer hydrogen-bonding bottlenecks in the open state than in the closed state. Thus, faster dynamics and higher orientational order of water molecules in the open channel establish the water network structure that is necessary for proton hopping.

Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics

Computational approaches are becoming an essential tool in modern drug design and discovery, with fast compound triaging using a combination of machine learning and docking techniques followed by molecular dynamics binding free energies assessment using alchemical techniques. The traditional MD-based alchemical free energy perturbation (FEP) method faces severe sampling issues that may limits its reliability in automated workflows. Here we review the major sources of uncertainty in FEP protocols for drug discovery, showing how the sampling problem can be effectively tackled by switching to nonequilibrium alchemical techniques.

Multimodal Response to Copper Binding in Superoxide Dismutase Dynamics

Copper/zinc superoxide dismutase (SOD) is a homodimeric metalloenzyme that has been extensively studied as a benchmark for structure-function relationships in proteins, in particular because of its implication in the familial form of the neurodegenerative disease amyotrophic lateral sclerosis. Here, we investigate microcrystalline preparations of two differently metalated forms of SOD, namely, the fully mature functional Cu,Zn state and the E,Zn-SOD state in which the Cu site is empty. By using solid-state NMR with fast magic-angle spinning (MAS) at high magnetic fields (¹H Larmor frequency of 800-1000 MHz), we quantify motions spanning a dynamic range from ns to ms. We determine that metal ion uptake does not act as a rigidification element but as a switch redistributing motional processes on different time scales, with coupling of the dynamics of histidine side chains and those of remote key backbone elements of the protein.

Recent advances in solid-state relaxation dispersion techniques

This review describes two rotating-frame (R_1ρ) relaxation dispersion methods, namely the Bloch-McConnell Relaxation Dispersion and the Near-rotary Resonance Relaxation Dispersion, which enable the study of microsecond time-scale conformational fluctuations in the solid state using magic-angle-spinning nuclear magnetic resonance spectroscopy. The goal is to provide the reader with key ideas, experimental descriptions, and practical considerations associated with R_1ρ measurements that are needed for analyzing relaxation dispersion and quantifying conformational exchange. While the focus is on protein motion, many presented concepts can be equally well adapted to study the microsecond time-scale dynamics of other bio- (e.g. lipids, polysaccharides, nucleic acids), organic (e.g. pharmaceutical compounds), or inorganic molecules (e.g., metal organic frameworks). This article summarizes the essential contributions made by recent theoretical and experimental solid-state NMR studies to our understanding of protein motion. Here we discuss recent advances in fast MAS applications that enable the observation and atomic level characterization of sparsely populated conformational states which are otherwise inaccessible for other experimental methods. Such high-energy states are often associated with protein functions such as molecular recognition, ligand binding, or enzymatic catalysis, as well as with disease-related properties such as misfolding and amyloid formation.

Protein Motional Details Revealed by Complementary Structural Biology Techniques

Proteins depend on defined molecular plasticity for their functionality. How to comprehensively capture dynamics correctly is of ubiquitous biological importance. Approaches commonly used to probe protein dynamics include model-free elucidation of site-specific motion by NMR relaxation, molecular dynamics (MD)-based approaches, and capturing the substates within a dynamic ensemble by recent eNOE-based multiple-structure approaches. Even though MD is sometimes combined with ensemble-averaged NMR restraints, these approaches have largely been developed and used individually. Owing to the different underlying concepts and practical requirements, it has remained unclear how they compare, and how they cross-validate and complement each other. Here, we extract and compare the differential information contents of MD simulations, NMR relaxation measurements, and eNOE-based multi-state structures for the SH3 domain of chicken α-spectrin. The data show that a validated, consistent, and detailed picture is feasible both for timescales and actual conformational states sampled in the dynamic ensemble. This includes the biologically important side-chain plasticity, for which experimentally cross-validated assessment is a significant challenge.

Simultaneous recording of intra- and inter-residue linking experiments for backbone assignments in proteins at MAS frequencies higher than 60 kHz

Obtaining site-specific assignments for the NMR spectra of proteins in the solid state is a significant bottleneck in deciphering their biophysics. This is primarily due to the time-intensive nature of the experiments. Additionally, the low resolution in the [Formula: see text]-dimension requires multiple complementary experiments to be recorded to lift degeneracies in assignments. We present here an approach, gleaned from the techniques used in multiple-acquisition experiments, which allows the recording of forward and backward residue-linking experiments in a single experimental block. Spectra from six additional pathways are also recovered from the same experimental block, without increasing the probe duty cycle. These experiments give intra- and inter residue connectivities for the backbone [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] resonances and should alone be sufficient to assign these nuclei in proteins at MAS frequencies > 60 kHz. The validity of this approach is tested with experiments on a standard tripeptide N-formyl methionyl-leucine-phenylalanine (f-MLF) at a MAS frequency of 62.5 kHz, which is also used as a test-case for determining the sensitivity of each of the experiments. We expect this approach to have an immediate impact on the way assignments are obtained at MAS frequencies [Formula: see text].

Enhancing NMR derived ensembles with kinetics on multiple timescales

Nuclear magnetic resonance (NMR) has the unique advantage of elucidating the structure and dynamics of biomolecules in solution at physiological temperatures, where they are in constant movement on timescales from picoseconds to milliseconds. Such motions have been shown to be critical for enzyme catalysis, allosteric regulation, and molecular recognition. With NMR being particularly sensitive to these timescales, detailed information about the kinetics can be acquired. However, nearly all methods of NMR-based biomolecular structure determination neglect kinetics, which introduces a large approximation to the underlying physics, limiting both structural resolution and the ability to accurately determine molecular flexibility. Here we present the Kinetic Ensemble approach that uses a hierarchy of interconversion rates between a set of ensemble members to rigorously calculate Nuclear Overhauser Effect (NOE) intensities. It can be used to simultaneously refine both temporal and structural coordinates. By generalizing ideas from the extended model free approach, the method can analyze the amplitudes and kinetics of motions anywhere along the backbone or side chains. Furthermore, analysis of a large set of crystal structures suggests that NOE data contains a surprising amount of high-resolution information that is better modeled using our approach. The Kinetic Ensemble approach provides the means to unify numerous types of experiments under a single quantitative framework and more fully characterize and exploit kinetically distinct protein states. While we apply the approach here to the protein ubiquitin and cross validate it with previously derived datasets, the approach can be applied to any protein for which NOE data is available.

Improving the quality of oriented membrane protein spectra using heat-compensated separated local field experiments

Oriented sample solid-state NMR (OS-ssNMR) spectroscopy is a powerful technique to determine the topology of membrane proteins in oriented lipid bilayers. Separated local field (SLF) experiments are central to this technique as they provide first-order orientational restraints, i.e., dipolar couplings and anisotropic chemical shifts. Despite the use of low-E (or E-free) probes, the heat generated during the execution of 2D and 3D SLF pulse sequences causes sizeable line-shape distortions. Here, we propose a new heat-compensated SE-SAMPI4 (hcSE-SAMPI4) pulse sequence that holds the temperature constant for the duration of the experiment. This modification of the SE-SAMPI4 results in sharper and more intense resonances without line-shape distortions. The spectral improvements are even more apparent when paramagnetic relaxation agents are used to speed up data collection. We tested the hcSE-SAMPI4 pulse sequence on a single-span membrane protein, sarcolipin (SLN), reconstituted in magnetically aligned lipid bicelles. In addition to eliminating peak distortions, the hcSE-SAMPI4 experiment increased the average signal-to-noise ratio by 20% with respect to the original SE-SAMPI4.

Quantifying Microsecond Exchange in Large Protein Complexes with Accelerated Relaxation Dispersion Experiments in the Solid State

Solid state NMR is a powerful method to obtain information on the structure and dynamics of protein complexes that, due to solubility and size limitations, cannot be achieved by other methods. Here, we present an approach that allows the quantification of microsecond conformational exchange in large protein complexes by using a paramagnetic agent to accelerate ¹⁵N R_1ρ relaxation dispersion measurements and overcome sensitivity limitations. The method is validated on crystalline GB1 and then applied to a >300 kDa precipitated complex of GB1 with full length human immunoglobulin G (IgG). The addition of a paramagnetic agent increased the signal to noise ratio per time unit by a factor of 5, which allowed full relaxation dispersion curves to be recorded on a sample containing less than 50 μg of labelled material in 5 and 10 days on 850 and 700 MHz spectrometers, respectively. We discover a similar exchange process across the β-sheet in GB1 in crystals and in complex with IgG. However, the slow motion observed for a number of residues in the α-helix of crystalline GB1 is not detected in the complex.

Exact distance measurements for structure and dynamics in solid proteins by fast-magic-angle-spinning NMR

Fast-magic-angle-spinning solid-state NMR is a developing technique for determination of protein structure and dynamics. Proton-proton correlations usually lead to rough distance restraints, a serious hurdle towards high-resolution structures. Analogous to the "eNOE" concept in solution, an integrative approach for more accurate restraints enables improved structural accuracy with minimal analytical effort.